Unraveling the Ancient Introgression History of Xanthoceras (Sapindaceae): Insights from Phylogenomic Analysis

Ancient introgression is an infrequent evolutionary process often associated with conflicts between nuclear and organellar phylogenies. Determining whether such conflicts arise from introgression, incomplete lineage sorting (ILS), or other processes is essential to understanding plant diversification. Previous studies have reported phylogenetic discordance in the placement of <i>Xanthoceras</i>, but its causes remain unclear. Here, we analyzed transcriptome data from 41 Sapindaceae samples to reconstruct phylogenies and investigate this discordance. While nuclear phylogenies consistently placed <i>Xanthoceras</i> as sister to subfam. Hippocastanoideae, plastid data positioned it as the earliest-diverging lineage within Sapindaceae. Our coalescent simulations suggest that this cyto-nuclear discordance is unlikely to be explained by ILS alone. HyDe and PhyloNet analyses provided strong evidence that <i>Xanthoceras</i> experienced ancient introgression, incorporating approximately 16% of its genetic material from ancestral subfam. Sapindoideae lineages. Morphological traits further support this evolutionary history, reflecting characteristics of both contributing subfamilies. Likely occurring during the Paleogene, this introgression represents a rare instance of cross-subfamily gene flow shaping the evolutionary trajectory of a major plant lineage. Our findings clarify the evolutionary history of <i>Xanthoceras</i> and underscore the role of ancient introgression in driving phylogenetic conflicts, offering a rare example of introgression-driven diversification in angiosperms.